PROTAC chemical probes for histone deacetylase enzymes

Replacing a Cereblon Ligand by a DDB1 and CUL4 Associated Factor 11 (DCAF11) Recruiter Converts a Selective Histone Deacetylase 6 PROTAC into a Pan-Degrader

Proteolysis-targeting chimeras (PROTACs) have recently gained popularity as targeted protein degradation (TPD) promises to overcome the limitations of occupancy-driven pharmacology. However, most degraders rely on a small number of E3 ligases. In this study, we present the first-in-class histone deacetylase (HDAC) PROTACs recruiting the DDB1- and CUL4- associated factor 11 (DCAF11). We established a synthesis route entirely on solid-phase to prepare a set of eleven degraders. The long and flexible spacer bearing FF2039 (1j) showed significant HDAC1 and 6 degradation in combination with cytotoxicity against the multiple myeloma cell line MM.1S. Further investigations revealed that 1j was also able to degrade HDAC isoforms of class I, IIa and IIb. Compared to our previously published cereblon-recruiting HDAC6 selective PROTAC A6, we succesfully transformed the selective degrader into a pan-HDAC degrader by switching the recruited E3 ligase. A detailed profiling of the anticancer properties of 1j demonstrated its significant antiproliferative activity against both hematological and solid cancer cell lines, driven by cell cycle arrest and apoptosis induction.

Design, synthesis and evaluation of pyrrolobenzodiazepine (PBD)-based PROTAC conjugates for the selective degradation of the NF-κB RelA/p65 subunit

NF-κB signalling is frequently dysregulated in human cancers making it an attractive therapeutic target. Despite concerted efforts to generate NF-κB inhibitors, direct pharmacological inhibition of the kinases mediating canonical NF-κB has failed due to on-target toxicities in normal tissues. So, alternative strategies, designed to target specific components of the NF-κB signalling machinery, have the potential to selectively inhibit tumour cells whilst reducing the toxicities associated with broad inhibition of NF-κB in non-malignant cells. Here we present evidence that a C8-linked pyrrolobenzodiazepine (PBD) containing proteolysis-targeting chimera (PROTAC) selectively degrades the NF-κB subunit, RelA/p65, in a proteasome-dependent manner. Our lead PROTAC (JP-163-16, 15d) showed cytotoxicity with mean LC50 values of 2.9 μM in MDA-MB-231 cells, 0.14 μM in MEC-1 cells and 0.23 μM in primary chronic lymphocytic leukaemia cells. In contrast, 15d was two-logs less toxic in primary B- and T-lymphocytes (mean LD50 19.1 μM and 36.4 μM, respectively). Importantly, the development of 15d, by conjugating the C8-linked PBD with a cereblon-targeting ligand using a five-carbon linker, abolished the ability of the C8-linked PBD to bind to DNA, whilst demonstrating cytotoxicity in cancer cells associated with the degradation of RelA/p65. Mechanistically, 15d displayed PROTAC credentials through the selective degradation of NF-κB RelA/p65 in a proteasome-dependent manner and showed a five-fold reduction in potency in the cereblon deficient, lenalidomide resistant, myeloma cell line, RPMI-8226. To our knowledge, this work describes the first PROTAC capable of selective degradation of a single NF-κB subunit and highlights the therapeutic potential of our strategy for the treatment of RelA/p65-dependent tumours.

Epigenetic drugs in cancer therapy

Genetic and epigenetic modifications of DNA are involved in cancer initiation and progression. Epigenetic modifications change chromatin structure and DNA accessibility and thus affect DNA replication, DNA repair and transcription. Epigenetic modifications are reversible and include DNA methylation, histone acetylation and histone methylation. DNA methylation is catalysed by DNA methyltransferases, histone acetylation and deacetylation are catalysed by histone acetylases and deacetylases, while histone methylation is catalysed by histone methyltransferases. Epigenetic modifications are dysregulated in several cancers, making them cancer therapeutic targets. Epigenetic drugs (epi-drugs) which are inhibitors of epigenetic modifications and include DNA methyltransferase inhibitors (DNMTi), histone deacetylase inhibitors (HDACi), histone methyltransferase inhibitors (HMTi) and bromodomain and extra-terminal motif protein inhibitors (BETi), have demonstrated clinical success as anti-cancer agents. Furthermore, the combination of epi-drugs with standard chemotherapeutic agents has demonstrated promising anti-cancer effects in pre-clinical and clinical settings. In this review, we discuss the role of epi-drugs in cancer therapy and explore their current and future use in combination with other anti-cancer agents used in the clinic. We further highlight the side effects and limitations of epi-drugs. We additionally discuss novel delivery methods and novel tumour epigenetic biomarkers for the screening, diagnosis and development of personalised cancer treatments, in order to reduce off-target toxicity and improve the specificity and anti-tumour efficacy of epi-drugs.

Development of the First-in-Class FEM1B-Recruiting Histone Deacetylase Degraders

Targeted protein degradation (TPD) represents a promising alternative to conventional occupancy-driven protein inhibition. Despite the existence of more than 600 E3 ligases in the human proteome, so far only a few have been utilized for TPD of histone deacetylases (HDACs), which represent important epigenetic anticancer drug targets. In this study, we disclose the first-in-class Fem-1 homologue B (FEM1B)-recruiting HDAC degraders. A set of 12 proteolysis targeting chimeras (PROTACs) was synthesized using a solid-phase supported parallel synthesis approach utilizing a covalent FEM1B ligand as an E3 ligase warhead. The evaluation of the HDAC degradation efficiency revealed substantial HDAC1 degradation by the top-performing degrader FF2049 (1g: Dmax = 85%; DC50 = 257 nM). Unlike our previously published cereblon-recruiting selective HDAC6 degrader, A6, which uses the same HDAC ligand, the FEM1B-based PROTACs achieved selective HDAC1-3 degradation. This unexpected change in the HDAC isoform degradation profile was accompanied by significant enhancement of the antiproliferative properties.

Stimuli-responsive prodrugs with self-immolative linker for improved cancer therapy

Self-immolative prodrugs have gained significant attention as an innovative approach for targeted cancer therapy. These prodrugs are engineered to release the active anticancer agents in response to specific triggers within the tumor microenvironment, thereby improving therapeutic precision while reducing systemic toxicity. This review focuses on the molecular architecture and design principles of self-immolative prodrugs, emphasizing the role of stimuli-responsive linkers and activation mechanisms that enable controlled drug release. Recent advancements in this field include the development of prodrugs that incorporate targeting moieties for enhanced site-specificity. Moreover, the review discusses the incorporation of targeting moieties to achieve site-specific drug delivery, thereby improving the selectivity of treatment. By summarizing key research from the past five years, this review highlights the potential of self-immolative prodrugs to revolutionize cancer treatment strategies and pave the way for their integration into clinical practice.

Probing class I histone deacetylases (HDAC) with proteolysis targeting chimera (PROTAC) for the development of highly potent and selective degraders

Class I HDACs are considered promising targets for cancer due to their role in epigenetic modifications. The main challenges in developing a new, potent and non-toxic class I HDAC inhibitor are selectivity and appropriate pharmacokinetics. The PROTAC technique (Proteolysis Targeting Chimera) is a new method in drug development for the production of active substances that can degrade a protein of interest (POI) instead of inhibiting it. This technique will open the era to produce selective and potent drugs with a high margin of safety. Previously, we reported different inhibitors targeting class I HDACs functionalized with aminobenzamide or hydroxamate groups. In the current research work, we will employ PROTAC technique to develop class I HDAC degraders based on our previously reported inhibitors. We synthesized two series of aminobenzamide-based PROTACs and hydroxamate-based PROTACs and tested them in vitro against class I HDACs. To ensure their degradation, all of them were screened against HDAC2 as representative example of class I. The best candidates were evaluated at different concentrations at various HDAC subtypes. This resulted in the PROTAC (32a) (HI31.1) that degrades HDAC8 with a DC50 of 8.9 nM with a proper margin of selectivity against other isozymes. Moreover, PROTAC 32a is able to degrade HDAC6 with DC50 = 14.3 nM. Apoptotic study on leukemic cells (MV-4-11) displayed more than 50 % apoptosis took place at 100 nM. PROTAC 32a (HI31.1) showed a good margin of safety against normal cell line and proper chemical stability.

Cereblon-recruiting proteolysis targeting chimeras (PROTACs) can determine the selective degradation of HDAC1 over HDAC3

Histone deacetylase (HDAC) enzymes 1-3 exist in several corepressor complexes and are viable drug targets. To date, proteolysis targeting chimeras (PROTACs) designed to target HDAC1-3 typically exhibit the selective degradation of HDAC3. Herein, we report cereblon-recruiting PROTACs that degrade HDAC1 with selectivity over HDAC3.

Correction: Curcio et al. The Histone Deacetylase Family: Structural Features and Application of Combined Computational Methods. Pharmaceuticals 2024, 17, 620

In the original publication [...].

Targeted Protein Degradation (TPD) for Immunotherapy: Understanding Proteolysis Targeting Chimera-Driven Ubiquitin-Proteasome Interactions

Targeted protein degradation or TPD, is rapidly emerging as a treatment that utilizes small molecules to degrade proteins that cause diseases. TPD allows for the selective removal of disease-causing proteins, including proteasome-mediated degradation, lysosome-mediated degradation, and autophagy-mediated degradation. This approach has shown great promise in preclinical studies and is now being translated to treat numerous diseases, including neurodegenerative diseases, infectious diseases, and cancer. This review discusses the latest advances in TPD and its potential as a new chemical modality for immunotherapy, with a special focus on the innovative applications and cutting-edge research of PROTACs (Proteolysis TArgeting Chimeras) and their efficient translation from scientific discovery to technological achievements. Our review also addresses the significant obstacles and potential prospects in this domain, while also offering insights into the future of TPD for immunotherapeutic applications.

MDM2 Antagonist Idasanutlin Reduces HDAC1/2 Abundance and Corepressor Partners but Not HDAC3

Histone deacetylases 1-3 (HDAC1, HDAC2, and HDAC3) and their associated corepressor complexes play important roles in regulating chromatin structure and gene transcription. HDAC enzymes are also validated drug targets for oncology and offer promise toward new drugs for neurodegenerative diseases and cardiovascular diseases. We synthesized four novel heterobifunctional molecules designed to recruit the mouse double minute 2 homologue (MDM2) E3 ligase to degrade HDAC1-3 utilizing the MDM2 inhibitor idasanutlin, known as proteolysis targeting chimeras (PROTACs). Idasanutlin inhibits the MDM2-P53 protein-protein interaction and is in clinical trials. Although two MDM2-recruiting heterobifunctional molecules reduced HDAC1 and HDAC2 abundance with complete selectivity over HDAC3 and reduced HDAC1/2 corepressor components LSD1 and SIN3A, we were surprised to observe that idasanutlin alone was also capable of this effect. This finding suggests an association between the MDM2 E3 ligase and HDAC1/2 corepressor complexes, which could be important for designing future dual/bifunctional HDAC- and MDM2-targeting therapeutics, such as PROTACs.